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molgenis/molgenis | molgenis-semantic-mapper/src/main/java/org/molgenis/semanticmapper/controller/MappingServiceController.java | MappingServiceController.deleteMappingProject | @PostMapping("/removeMappingProject")
public String deleteMappingProject(@RequestParam() String mappingProjectId) {
MappingProject project = mappingService.getMappingProject(mappingProjectId);
LOG.info("Deleting mappingProject {}", project.getName());
mappingService.deleteMappingProject(mappingProjectId);... | java | @PostMapping("/removeMappingProject")
public String deleteMappingProject(@RequestParam() String mappingProjectId) {
MappingProject project = mappingService.getMappingProject(mappingProjectId);
LOG.info("Deleting mappingProject {}", project.getName());
mappingService.deleteMappingProject(mappingProjectId);... | [
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molgenis/molgenis | molgenis-semantic-mapper/src/main/java/org/molgenis/semanticmapper/controller/MappingServiceController.java | MappingServiceController.removeAttributeMapping | @PostMapping("/removeAttributeMapping")
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MappingProject project = mappingService.getMappingProject(mappingProjectI... | java | @PostMapping("/removeAttributeMapping")
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molgenis/molgenis | molgenis-semantic-mapper/src/main/java/org/molgenis/semanticmapper/controller/MappingServiceController.java | MappingServiceController.viewMappingProject | @GetMapping("/mappingproject/{id}")
public String viewMappingProject(@PathVariable("id") String identifier, Model model) {
MappingProject project = mappingService.getMappingProject(identifier);
MappingTarget mappingTarget = project.getMappingTargets().get(0);
String target = mappingTarget.getName();
m... | java | @GetMapping("/mappingproject/{id}")
public String viewMappingProject(@PathVariable("id") String identifier, Model model) {
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molgenis/molgenis | molgenis-semantic-mapper/src/main/java/org/molgenis/semanticmapper/controller/MappingServiceController.java | MappingServiceController.autoGenerateAlgorithms | void autoGenerateAlgorithms(
EntityMapping mapping,
EntityType sourceEntityType,
EntityType targetEntityType,
MappingProject project) {
algorithmService.autoGenerateAlgorithm(sourceEntityType, targetEntityType, mapping);
mappingService.updateMappingProject(project);
} | java | void autoGenerateAlgorithms(
EntityMapping mapping,
EntityType sourceEntityType,
EntityType targetEntityType,
MappingProject project) {
algorithmService.autoGenerateAlgorithm(sourceEntityType, targetEntityType, mapping);
mappingService.updateMappingProject(project);
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molgenis/molgenis | molgenis-semantic-mapper/src/main/java/org/molgenis/semanticmapper/controller/MappingServiceController.java | MappingServiceController.getNewSources | private List<EntityType> getNewSources(MappingTarget target) {
return dataService
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.filter(name -> isValidSource(target, name))
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return dataService
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molgenis/molgenis | molgenis-swagger/src/main/java/org/molgenis/swagger/controller/SwaggerController.java | SwaggerController.init | @GetMapping
public String init(Model model) {
final UriComponents uriComponents =
ServletUriComponentsBuilder.fromCurrentContextPath().build();
model.addAttribute("molgenisUrl", uriComponents.toUriString() + URI + "/swagger.yml");
model.addAttribute("baseUrl", uriComponents.toUriString());
f... | java | @GetMapping
public String init(Model model) {
final UriComponents uriComponents =
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model.addAttribute("molgenisUrl", uriComponents.toUriString() + URI + "/swagger.yml");
model.addAttribute("baseUrl", uriComponents.toUriString());
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molgenis/molgenis | molgenis-swagger/src/main/java/org/molgenis/swagger/controller/SwaggerController.java | SwaggerController.swagger | @GetMapping(value = "/swagger.yml", produces = "text/yaml")
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molgenis/molgenis | molgenis-i18n/src/main/java/org/molgenis/i18n/I18nUtils.java | I18nUtils.getLanguageCode | public static String getLanguageCode(String name) {
if (!isI18n(name)) return null;
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if (!isI18n(name)) return null;
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molgenis/molgenis | molgenis-python/src/main/java/org/molgenis/python/PythonScriptExecutor.java | PythonScriptExecutor.executeScript | public void executeScript(String pythonScript, PythonOutputHandler outputHandler) {
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// Check if Python is installed
File file = new File(pythonScriptExecutable);
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molgenis/molgenis | molgenis-api-data/src/main/java/org/molgenis/api/data/RestService.java | RestService.toEntity | public Entity toEntity(final EntityType meta, final Map<String, Object> request) {
final Entity entity = entityManager.create(meta, POPULATE);
for (Attribute attr : meta.getAtomicAttributes()) {
if (attr.getExpression() == null) {
String paramName = attr.getName();
if (request.containsKey... | java | public Entity toEntity(final EntityType meta, final Map<String, Object> request) {
final Entity entity = entityManager.create(meta, POPULATE);
for (Attribute attr : meta.getAtomicAttributes()) {
if (attr.getExpression() == null) {
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molgenis/molgenis | molgenis-api-data/src/main/java/org/molgenis/api/data/RestService.java | RestService.toEntityValue | public Object toEntityValue(Attribute attr, Object paramValue, Object id) {
// Treat empty strings as null
if ((paramValue instanceof String) && ((String) paramValue).isEmpty()) {
paramValue = null;
}
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AttributeType attrType = attr.getDataType();
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// Treat empty strings as null
if ((paramValue instanceof String) && ((String) paramValue).isEmpty()) {
paramValue = null;
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molgenis/molgenis | molgenis-validation/src/main/java/org/molgenis/validation/JsonValidator.java | JsonValidator.loadSchema | public Schema loadSchema(String schema) {
try {
JSONObject rawSchema = new JSONObject(new JSONTokener(schema));
return SchemaLoader.load(rawSchema);
} catch (JSONException | SchemaException e) {
throw new InvalidJsonSchemaException(e);
}
} | java | public Schema loadSchema(String schema) {
try {
JSONObject rawSchema = new JSONObject(new JSONTokener(schema));
return SchemaLoader.load(rawSchema);
} catch (JSONException | SchemaException e) {
throw new InvalidJsonSchemaException(e);
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molgenis/molgenis | molgenis-validation/src/main/java/org/molgenis/validation/JsonValidator.java | JsonValidator.validate | public void validate(String json, String schemaJson) {
Schema schema = loadSchema(schemaJson);
validate(json, schema);
} | java | public void validate(String json, String schemaJson) {
Schema schema = loadSchema(schemaJson);
validate(json, schema);
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molgenis/molgenis | molgenis-data-elasticsearch/src/main/java/org/molgenis/data/elasticsearch/generator/QueryGenerator.java | QueryGenerator.nestedQueryBuilder | private QueryBuilder nestedQueryBuilder(
List<Attribute> attributePath, QueryBuilder queryBuilder) {
if (attributePath.size() == 1) {
return queryBuilder;
} else if (attributePath.size() == 2) {
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getQueryFieldName(attributePath.get(0)), queryBuilder, ... | java | private QueryBuilder nestedQueryBuilder(
List<Attribute> attributePath, QueryBuilder queryBuilder) {
if (attributePath.size() == 1) {
return queryBuilder;
} else if (attributePath.size() == 2) {
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molgenis/molgenis | molgenis-ontology/src/main/java/org/molgenis/ontology/sorta/controller/Href.java | Href.concatAttributeHref | public static String concatAttributeHref(
String baseUri, String qualifiedEntityName, Object entityIdValue, String attributeName) {
return String.format(
"%s/%s/%s/%s",
baseUri,
encodePathSegment(qualifiedEntityName),
encodePathSegment(DataConverter.toString(entityIdValue)),
... | java | public static String concatAttributeHref(
String baseUri, String qualifiedEntityName, Object entityIdValue, String attributeName) {
return String.format(
"%s/%s/%s/%s",
baseUri,
encodePathSegment(qualifiedEntityName),
encodePathSegment(DataConverter.toString(entityIdValue)),
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molgenis/molgenis | molgenis-ontology/src/main/java/org/molgenis/ontology/sorta/controller/Href.java | Href.concatMetaAttributeHref | public static String concatMetaAttributeHref(
String baseUri, String entityParentName, String attributeName) {
return String.format(
"%s/%s/meta/%s",
baseUri, encodePathSegment(entityParentName), encodePathSegment(attributeName));
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String baseUri, String entityParentName, String attributeName) {
return String.format(
"%s/%s/meta/%s",
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molgenis/molgenis | molgenis-ontology/src/main/java/org/molgenis/ontology/sorta/controller/Href.java | Href.concatEntityHref | public static String concatEntityHref(
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qualifiedEntityName = "";
}
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if (null == qualifiedEntityName) {
qualifiedEntityName = "";
}
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molgenis/molgenis | molgenis-ontology/src/main/java/org/molgenis/ontology/sorta/controller/Href.java | Href.concatMetaEntityHref | public static String concatMetaEntityHref(String baseUri, String qualifiedEntityName) {
return String.format("%s/%s/meta", baseUri, encodePathSegment(qualifiedEntityName));
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molgenis/molgenis | molgenis-ontology/src/main/java/org/molgenis/ontology/sorta/controller/Href.java | Href.concatEntityCollectionHref | public static String concatEntityCollectionHref(
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String ids;
ids = entitiesIds.stream().map(Href::encodeIdToRSQL).collect(Collectors.joining(","));
return String.format(
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String ids;
ids = entitiesIds.stream().map(Href::encodeIdToRSQL).collect(Collectors.joining(","));
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molgenis/molgenis | molgenis-data-import/src/main/java/org/molgenis/data/export/EmxExportServiceImpl.java | EmxExportServiceImpl.export | @Override
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Progress progress) {
requireNonNull(progress);
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tr... | java | @Override
@Transactional(readOnly = true, isolation = Isolation.SERIALIZABLE)
public void export(
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Path downloadFilePath,
Progress progress) {
requireNonNull(progress);
if (!(entityTypes.isEmpty() && packages.isEmpty())) {
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molgenis/molgenis | molgenis-data-import/src/main/java/org/molgenis/data/export/EmxExportServiceImpl.java | EmxExportServiceImpl.writeEntityTypes | void writeEntityTypes(Collection<EntityType> entityTypes, XlsxWriter writer) {
LinkedList<EntityType> sortedEntityTypes = sortEntityTypesAbstractFirst(entityTypes);
if (!writer.hasSheet(EMX_ENTITIES)) {
writer.createSheet(EMX_ENTITIES, newArrayList(ENTITIES_ATTRS.keySet()));
}
writer.writeRows(sor... | java | void writeEntityTypes(Collection<EntityType> entityTypes, XlsxWriter writer) {
LinkedList<EntityType> sortedEntityTypes = sortEntityTypesAbstractFirst(entityTypes);
if (!writer.hasSheet(EMX_ENTITIES)) {
writer.createSheet(EMX_ENTITIES, newArrayList(ENTITIES_ATTRS.keySet()));
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/QueryUtils.java | QueryUtils.getQueryRuleAttribute | public static Attribute getQueryRuleAttribute(QueryRule queryRule, EntityType entityType) {
String queryRuleField = queryRule.getField();
if (queryRuleField == null) {
return null;
}
Attribute attr = null;
String[] queryRuleFieldTokens = StringUtils.split(queryRuleField, NESTED_ATTRIBUTE_SEPA... | java | public static Attribute getQueryRuleAttribute(QueryRule queryRule, EntityType entityType) {
String queryRuleField = queryRule.getField();
if (queryRuleField == null) {
return null;
}
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String[] queryRuleFieldTokens = StringUtils.split(queryRuleField, NESTED_ATTRIBUTE_SEPA... | [
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/EntityTypeDependencyResolver.java | EntityTypeDependencyResolver.getDependencies | private static Function<EntityTypeNode, Set<EntityTypeNode>> getDependencies() {
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// get referenced entities excluding entities of mappedBy attributes
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// get referenced entities excluding entities of mappedBy attributes
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/EntityTypeDependencyResolver.java | EntityTypeDependencyResolver.expandEntityTypeDependencies | private static Set<EntityTypeNode> expandEntityTypeDependencies(EntityTypeNode entityTypeNode) {
if (LOG.isTraceEnabled()) {
LOG.trace(
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entityTypeNode.getEntityType().getId(),
entityTypeNo... | java | private static Set<EntityTypeNode> expandEntityTypeDependencies(EntityTypeNode entityTypeNode) {
if (LOG.isTraceEnabled()) {
LOG.trace(
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entityTypeNo... | [
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molgenis/molgenis | molgenis-security/src/main/java/org/molgenis/security/twofactor/auth/TwoFactorAuthenticationFilter.java | TwoFactorAuthenticationFilter.hasAuthenticatedMolgenisToken | private boolean hasAuthenticatedMolgenisToken() {
boolean hasAuthenticatedMolgenisToken = false;
Authentication authentication = SecurityContextHolder.getContext().getAuthentication();
if (authentication instanceof RestAuthenticationToken) {
hasAuthenticatedMolgenisToken = authentication.isAuthenticat... | java | private boolean hasAuthenticatedMolgenisToken() {
boolean hasAuthenticatedMolgenisToken = false;
Authentication authentication = SecurityContextHolder.getContext().getAuthentication();
if (authentication instanceof RestAuthenticationToken) {
hasAuthenticatedMolgenisToken = authentication.isAuthenticat... | [
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/model/EntityType.java | EntityType.deepCopyAttributes | public static Map<String, Attribute> deepCopyAttributes(
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Map<String, Attribute> copiedAttributes = new LinkedHashMap<>();
// step #1: deep copy attributes
Map<String, Attribute> ownAttrMap =
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Map<String, Attribute> copiedAttributes = new LinkedHashMap<>();
// step #1: deep copy attributes
Map<String, Attribute> ownAttrMap =
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/model/EntityType.java | EntityType.getLabel | public String getLabel(String languageCode) {
String i18nLabel = getString(getI18nAttributeName(LABEL, languageCode));
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} | java | public String getLabel(String languageCode) {
String i18nLabel = getString(getI18nAttributeName(LABEL, languageCode));
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/model/EntityType.java | EntityType.getDescription | @Nullable
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@CheckForNull
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/model/EntityType.java | EntityType.getIdAttribute | public Attribute getIdAttribute() {
Attribute idAttr = getOwnIdAttribute();
if (idAttr == null) {
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if (extend != null) {
idAttr = extend.getIdAttribute();
}
}
return idAttr;
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Attribute idAttr = getOwnIdAttribute();
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}
}
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/model/EntityType.java | EntityType.getLabelAttribute | public Attribute getLabelAttribute() {
Attribute labelAttr = getOwnLabelAttribute();
if (labelAttr == null) {
EntityType extend = getExtends();
if (extend != null) {
labelAttr = extend.getLabelAttribute();
}
}
return labelAttr;
} | java | public Attribute getLabelAttribute() {
Attribute labelAttr = getOwnLabelAttribute();
if (labelAttr == null) {
EntityType extend = getExtends();
if (extend != null) {
labelAttr = extend.getLabelAttribute();
}
}
return labelAttr;
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/model/EntityType.java | EntityType.getLabelAttribute | public Attribute getLabelAttribute(String langCode) {
Attribute labelAttr = getLabelAttribute();
Attribute i18nLabelAttr =
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Attribute labelAttr = getLabelAttribute();
Attribute i18nLabelAttr =
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/model/EntityType.java | EntityType.getAttribute | public Attribute getAttribute(String attrName) {
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if (attr == null) {
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if (attr == null) {
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EntityType extendsEntityType = getExtends();
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/model/EntityType.java | EntityType.addSequenceNumber | static void addSequenceNumber(Attribute attr, Iterable<Attribute> attrs) {
Integer sequenceNumber = attr.getSequenceNumber();
if (null == sequenceNumber) {
int i =
stream(attrs)
.filter(a -> null != a.getSequenceNumber())
.mapToInt(Attribute::getSequenceNumber)
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if (null == sequenceNumber) {
int i =
stream(attrs)
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molgenis/molgenis | molgenis-data-i18n/src/main/java/org/molgenis/data/i18n/SystemEntityTypeI18nInitializer.java | SystemEntityTypeI18nInitializer.initialize | public void initialize(ContextRefreshedEvent event) {
ApplicationContext ctx = event.getApplicationContext();
Stream<String> languageCodes = LanguageService.getLanguageCodes();
EntityTypeMetadata entityTypeMeta = ctx.getBean(EntityTypeMetadata.class);
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ApplicationContext ctx = event.getApplicationContext();
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/populate/AutoValuePopulator.java | AutoValuePopulator.populate | public void populate(Entity entity) {
// auto date
generateAutoDateOrDateTime(singletonList(entity), entity.getEntityType().getAttributes());
// auto id
Attribute idAttr = entity.getEntityType().getIdAttribute();
if (idAttr != null
&& idAttr.isAuto()
&& entity.getIdValue() == null
... | java | public void populate(Entity entity) {
// auto date
generateAutoDateOrDateTime(singletonList(entity), entity.getEntityType().getAttributes());
// auto id
Attribute idAttr = entity.getEntityType().getIdAttribute();
if (idAttr != null
&& idAttr.isAuto()
&& entity.getIdValue() == null
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molgenis/molgenis | molgenis-data-i18n/src/main/java/org/molgenis/data/i18n/I18nPopulator.java | I18nPopulator.populateL10nStrings | public void populateL10nStrings() {
AllPropertiesMessageSource allPropertiesMessageSource = new AllPropertiesMessageSource();
String[] namespaces =
localizationMessageSources
.stream()
.map(PropertiesMessageSource::getNamespace)
.toArray(String[]::new);
allPropert... | java | public void populateL10nStrings() {
AllPropertiesMessageSource allPropertiesMessageSource = new AllPropertiesMessageSource();
String[] namespaces =
localizationMessageSources
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molgenis/molgenis | molgenis-data-i18n/src/main/java/org/molgenis/data/i18n/I18nPopulator.java | I18nPopulator.populateLanguages | public void populateLanguages() {
dataService.add(
LANGUAGE,
languageFactory.create(
LanguageService.DEFAULT_LANGUAGE_CODE, LanguageService.DEFAULT_LANGUAGE_NAME, true));
dataService.add(
LANGUAGE,
languageFactory.create("nl", new Locale("nl").getDisplayName(new Local... | java | public void populateLanguages() {
dataService.add(
LANGUAGE,
languageFactory.create(
LanguageService.DEFAULT_LANGUAGE_CODE, LanguageService.DEFAULT_LANGUAGE_NAME, true));
dataService.add(
LANGUAGE,
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molgenis/molgenis | molgenis-data-validation/src/main/java/org/molgenis/data/validation/ExpressionValidator.java | ExpressionValidator.resolveBooleanExpressions | List<Boolean> resolveBooleanExpressions(List<String> expressions, Entity entity) {
if (expressions.isEmpty()) {
return Collections.emptyList();
}
return jsMagmaScriptEvaluator
.eval(expressions, entity)
.stream()
.map(this::convertToBoolean)
.collect(toList());
} | java | List<Boolean> resolveBooleanExpressions(List<String> expressions, Entity entity) {
if (expressions.isEmpty()) {
return Collections.emptyList();
}
return jsMagmaScriptEvaluator
.eval(expressions, entity)
.stream()
.map(this::convertToBoolean)
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molgenis/molgenis | molgenis-core-ui/src/main/java/org/molgenis/core/ui/thememanager/ThemeManagerController.java | ThemeManagerController.addBootstrapTheme | @PreAuthorize("hasAnyRole('ROLE_SU')")
@PostMapping(value = "/add-bootstrap-theme")
public @ResponseBody Style addBootstrapTheme(
@RequestParam(value = "bootstrap3-style") MultipartFile bootstrap3Style,
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thro... | java | @PreAuthorize("hasAnyRole('ROLE_SU')")
@PostMapping(value = "/add-bootstrap-theme")
public @ResponseBody Style addBootstrapTheme(
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molgenis/molgenis | molgenis-util/src/main/java/org/molgenis/util/file/ZipFileUtil.java | ZipFileUtil.unzip | private static List<File> unzip(File file, NameMapper nameMapper) {
try {
File parentFile = file.getParentFile();
TrackingNameMapper trackingNameMapper = new TrackingNameMapper(parentFile, nameMapper);
ZipUtil.unpack(file, parentFile, trackingNameMapper);
return trackingNameMapper.getFiles()... | java | private static List<File> unzip(File file, NameMapper nameMapper) {
try {
File parentFile = file.getParentFile();
TrackingNameMapper trackingNameMapper = new TrackingNameMapper(parentFile, nameMapper);
ZipUtil.unpack(file, parentFile, trackingNameMapper);
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molgenis/molgenis | molgenis-semantic-search/src/main/java/org/molgenis/semanticsearch/string/NGramDistanceAlgorithm.java | NGramDistanceAlgorithm.createNGrams | public static Map<String, Integer> createNGrams(String inputQuery, boolean removeStopWords) {
List<String> wordsInString =
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if (removeStopWords) wordsInString.removeAll(STOPWORDSLIST);
List<String> stemmedWordsInString =
... | java | public static Map<String, Integer> createNGrams(String inputQuery, boolean removeStopWords) {
List<String> wordsInString =
Lists.newArrayList(Stemmer.replaceIllegalCharacter(inputQuery).split(" "));
if (removeStopWords) wordsInString.removeAll(STOPWORDSLIST);
List<String> stemmedWordsInString =
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molgenis/molgenis | molgenis-semantic-search/src/main/java/org/molgenis/semanticsearch/string/NGramDistanceAlgorithm.java | NGramDistanceAlgorithm.calculateScore | private static double calculateScore(
Map<String, Integer> inputStringTokens, Map<String, Integer> ontologyTermTokens) {
if (inputStringTokens.size() == 0 || ontologyTermTokens.size() == 0) return (double) 0;
int totalToken = getTotalNumTokens(inputStringTokens) + getTotalNumTokens(ontologyTermTokens);
... | java | private static double calculateScore(
Map<String, Integer> inputStringTokens, Map<String, Integer> ontologyTermTokens) {
if (inputStringTokens.size() == 0 || ontologyTermTokens.size() == 0) return (double) 0;
int totalToken = getTotalNumTokens(inputStringTokens) + getTotalNumTokens(ontologyTermTokens);
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molgenis/molgenis | molgenis-settings/src/main/java/org/molgenis/settings/DefaultSettingsEntity.java | DefaultSettingsEntity.addListener | public void addListener(SettingsEntityListener settingsEntityListener) {
RunAsSystemAspect.runAsSystem(
() ->
entityListenersService.addEntityListener(
entityTypeId,
new EntityListener() {
@Override
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RunAsSystemAspect.runAsSystem(
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entityTypeId,
new EntityListener() {
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] | b4d0d6b27e6f6c8d7505a3863dc03b589601f987 | https://github.com/molgenis/molgenis/blob/b4d0d6b27e6f6c8d7505a3863dc03b589601f987/molgenis-settings/src/main/java/org/molgenis/settings/DefaultSettingsEntity.java#L147-L163 | train |
molgenis/molgenis | molgenis-settings/src/main/java/org/molgenis/settings/DefaultSettingsEntity.java | DefaultSettingsEntity.removeListener | public void removeListener(SettingsEntityListener settingsEntityListener) {
RunAsSystemAspect.runAsSystem(
() ->
entityListenersService.removeEntityListener(
entityTypeId,
new EntityListener() {
@Override
public void postUpdate... | java | public void removeListener(SettingsEntityListener settingsEntityListener) {
RunAsSystemAspect.runAsSystem(
() ->
entityListenersService.removeEntityListener(
entityTypeId,
new EntityListener() {
@Override
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molgenis/molgenis | molgenis-data-excel/src/main/java/org/molgenis/data/excel/ExcelSheetWriter.java | ExcelSheetWriter.add | @Override
public void add(Entity entity) {
if (entity == null) throw new IllegalArgumentException("Entity cannot be null");
if (cachedAttributes == null)
throw new MolgenisDataException(
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Row poiRow = sh... | java | @Override
public void add(Entity entity) {
if (entity == null) throw new IllegalArgumentException("Entity cannot be null");
if (cachedAttributes == null)
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molgenis/molgenis | molgenis-data-excel/src/main/java/org/molgenis/data/excel/ExcelSheetWriter.java | ExcelSheetWriter.writeAttributeHeaders | public void writeAttributeHeaders(
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throw new IllegalArgumentException("AttributeWriteMode cannot be null")... | java | public void writeAttributeHeaders(
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molgenis/molgenis | molgenis-semantic-search/src/main/java/org/molgenis/semanticsearch/repository/TagRepository.java | TagRepository.getTagEntity | public Tag getTagEntity(String objectIRI, String label, Relation relation, String codeSystemIRI) {
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Tag tag =
dataService
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molgenis/molgenis | molgenis-bootstrap/src/main/java/org/molgenis/bootstrap/populate/RepositoryPopulator.java | RepositoryPopulator.populate | public boolean populate(ContextRefreshedEvent event) {
boolean databasePopulated = isDatabasePopulated();
if (!databasePopulated) {
LOG.trace("Populating database with I18N strings ...");
i18nPopulator.populateLanguages();
LOG.trace("Populated database with I18N strings");
}
LOG.trace... | java | public boolean populate(ContextRefreshedEvent event) {
boolean databasePopulated = isDatabasePopulated();
if (!databasePopulated) {
LOG.trace("Populating database with I18N strings ...");
i18nPopulator.populateLanguages();
LOG.trace("Populated database with I18N strings");
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molgenis/molgenis | molgenis-data-validation/src/main/java/org/molgenis/data/validation/QueryValidator.java | QueryValidator.validate | public void validate(Query<? extends Entity> query, EntityType entityType) {
query.getRules().forEach(queryRule -> validateQueryRule(queryRule, entityType));
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query.getRules().forEach(queryRule -> validateQueryRule(queryRule, entityType));
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/QueryRule.java | QueryRule.setValue | public void setValue(Object value) {
if (value instanceof Iterable<?>) {
this.value = stream((Iterable<?>) value).map(this::toValue).collect(toList());
} else {
this.value = toValue(value);
}
} | java | public void setValue(Object value) {
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molgenis/molgenis | molgenis-semantic-search/src/main/java/org/molgenis/semanticsearch/explain/service/ExplainServiceHelper.java | ExplainServiceHelper.findMatchedWords | Set<String> findMatchedWords(Explanation explanation) {
Set<String> words = new HashSet<>();
String description = explanation.getDescription();
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Set<String> words = new HashSet<>();
String description = explanation.getDescription();
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molgenis/molgenis | molgenis-semantic-search/src/main/java/org/molgenis/semanticsearch/explain/service/ExplainServiceHelper.java | ExplainServiceHelper.findMatchQueries | Map<String, Double> findMatchQueries(
String matchedWordsString, Map<String, String> collectExpandedQueryMap) {
Map<String, Double> qualifiedQueries = new HashMap<>();
Set<String> matchedWords = splitIntoTerms(matchedWordsString);
for (Entry<String, String> entry : collectExpandedQueryMap.entrySet()) ... | java | Map<String, Double> findMatchQueries(
String matchedWordsString, Map<String, String> collectExpandedQueryMap) {
Map<String, Double> qualifiedQueries = new HashMap<>();
Set<String> matchedWords = splitIntoTerms(matchedWordsString);
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molgenis/molgenis | molgenis-core-ui/src/main/java/org/molgenis/core/ui/controller/FeedbackController.java | FeedbackController.init | @Override
@GetMapping
public String init(final Model model) {
super.init(model);
model.addAttribute("adminEmails", userService.getSuEmailAddresses());
if (SecurityUtils.currentUserIsAuthenticated()) {
User currentUser = userService.getUser(SecurityUtils.getCurrentUsername());
if (currentUser... | java | @Override
@GetMapping
public String init(final Model model) {
super.init(model);
model.addAttribute("adminEmails", userService.getSuEmailAddresses());
if (SecurityUtils.currentUserIsAuthenticated()) {
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molgenis/molgenis | molgenis-core-ui/src/main/java/org/molgenis/core/ui/controller/FeedbackController.java | FeedbackController.createFeedbackMessage | @SuppressWarnings("squid:S3457") // do not use platform specific line ending
private SimpleMailMessage createFeedbackMessage(FeedbackForm form) {
SimpleMailMessage message = new SimpleMailMessage();
message.setTo(userService.getSuEmailAddresses().toArray(new String[] {}));
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mes... | java | @SuppressWarnings("squid:S3457") // do not use platform specific line ending
private SimpleMailMessage createFeedbackMessage(FeedbackForm form) {
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molgenis/molgenis | molgenis-core-ui/src/main/java/org/molgenis/core/ui/controller/FeedbackController.java | FeedbackController.getFormattedName | private static String getFormattedName(User user) {
List<String> parts = new ArrayList<>();
if (user.getTitle() != null) {
parts.add(user.getTitle());
}
if (user.getFirstName() != null) {
parts.add(user.getFirstName());
}
if (user.getMiddleNames() != null) {
parts.add(user.getM... | java | private static String getFormattedName(User user) {
List<String> parts = new ArrayList<>();
if (user.getTitle() != null) {
parts.add(user.getTitle());
}
if (user.getFirstName() != null) {
parts.add(user.getFirstName());
}
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/populate/IdGeneratorImpl.java | IdGeneratorImpl.generateRandomBytes | private byte[] generateRandomBytes(int nBytes, Random random) {
byte[] randomBytes = new byte[nBytes];
random.nextBytes(randomBytes);
return randomBytes;
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byte[] randomBytes = new byte[nBytes];
random.nextBytes(randomBytes);
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molgenis/molgenis | molgenis-jobs/src/main/java/org/molgenis/jobs/schedule/JobScheduler.java | JobScheduler.unschedule | synchronized void unschedule(String scheduledJobId) {
try {
quartzScheduler.deleteJob(new JobKey(scheduledJobId, SCHEDULED_JOB_GROUP));
} catch (SchedulerException e) {
String message = format("Error deleting ScheduledJob ''{0}''", scheduledJobId);
LOG.error(message, e);
throw new Schedu... | java | synchronized void unschedule(String scheduledJobId) {
try {
quartzScheduler.deleteJob(new JobKey(scheduledJobId, SCHEDULED_JOB_GROUP));
} catch (SchedulerException e) {
String message = format("Error deleting ScheduledJob ''{0}''", scheduledJobId);
LOG.error(message, e);
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molgenis/molgenis | molgenis-data-validation/src/main/java/org/molgenis/data/validation/meta/AttributeValidator.java | AttributeValidator.validateMappedBy | private static void validateMappedBy(Attribute attr, Attribute mappedByAttr) {
if (mappedByAttr != null) {
if (!isSingleReferenceType(mappedByAttr)) {
throw new MolgenisDataException(
format(
"Invalid mappedBy attribute [%s] data type [%s].",
mappedByAttr.ge... | java | private static void validateMappedBy(Attribute attr, Attribute mappedByAttr) {
if (mappedByAttr != null) {
if (!isSingleReferenceType(mappedByAttr)) {
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format(
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molgenis/molgenis | molgenis-data-validation/src/main/java/org/molgenis/data/validation/meta/AttributeValidator.java | AttributeValidator.validateOrderBy | private static void validateOrderBy(Attribute attr, Sort orderBy) {
if (orderBy != null) {
EntityType refEntity = attr.getRefEntity();
if (refEntity != null) {
for (Sort.Order orderClause : orderBy) {
String refAttrName = orderClause.getAttr();
if (refEntity.getAttribute(refA... | java | private static void validateOrderBy(Attribute attr, Sort orderBy) {
if (orderBy != null) {
EntityType refEntity = attr.getRefEntity();
if (refEntity != null) {
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molgenis/molgenis | molgenis-data-import/src/main/java/org/molgenis/data/importer/ImportServiceFactory.java | ImportServiceFactory.getImportService | public ImportService getImportService(File file, RepositoryCollection source) {
final Map<String, ImportService> importServicesMappedToExtensions = Maps.newHashMap();
importServices
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importServ... | java | public ImportService getImportService(File file, RepositoryCollection source) {
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importServices
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molgenis/molgenis | molgenis-semantic-search/src/main/java/org/molgenis/semanticsearch/string/Stemmer.java | Stemmer.cleanStemPhrase | public static String cleanStemPhrase(String phrase) {
StringBuilder stringBuilder = new StringBuilder();
for (String word : replaceIllegalCharacter(phrase).split(" ")) {
String stemmedWord = stem(word);
if (StringUtils.isNotEmpty(stemmedWord)) {
if (stringBuilder.length() > 0) {
st... | java | public static String cleanStemPhrase(String phrase) {
StringBuilder stringBuilder = new StringBuilder();
for (String word : replaceIllegalCharacter(phrase).split(" ")) {
String stemmedWord = stem(word);
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molgenis/molgenis | molgenis-ontology-core/src/main/java/org/molgenis/ontology/core/importer/repository/OntologyRepositoryCollection.java | OntologyRepositoryCollection.constructNodePath | private String constructNodePath(String parentNodePath, int currentPosition) {
StringBuilder nodePathStringBuilder = new StringBuilder();
if (!StringUtils.isEmpty(parentNodePath))
nodePathStringBuilder.append(parentNodePath).append('.');
nodePathStringBuilder
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.... | java | private String constructNodePath(String parentNodePath, int currentPosition) {
StringBuilder nodePathStringBuilder = new StringBuilder();
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nodePathStringBuilder
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/util/EntityUtils.java | EntityUtils.getTypedValue | public static Object getTypedValue(String valueStr, Attribute attr) {
// Reference types cannot be processed because we lack an entityManager in this route.
if (EntityTypeUtils.isReferenceType(attr)) {
throw new MolgenisDataException(
"getTypedValue(String, AttributeMetadata) can't be used for a... | java | public static Object getTypedValue(String valueStr, Attribute attr) {
// Reference types cannot be processed because we lack an entityManager in this route.
if (EntityTypeUtils.isReferenceType(attr)) {
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/util/EntityUtils.java | EntityUtils.getTypedValue | public static Object getTypedValue(String valueStr, Attribute attr, EntityManager entityManager) {
if (valueStr == null) return null;
switch (attr.getDataType()) {
case BOOL:
return Boolean.valueOf(valueStr);
case CATEGORICAL:
case FILE:
case XREF:
EntityType xrefEntity =... | java | public static Object getTypedValue(String valueStr, Attribute attr, EntityManager entityManager) {
if (valueStr == null) return null;
switch (attr.getDataType()) {
case BOOL:
return Boolean.valueOf(valueStr);
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/util/EntityUtils.java | EntityUtils.equalsEntities | public static boolean equalsEntities(
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List<Entity> attrs = newArrayList(entityIterable);
List<Entity> otherAttrs = newArrayList(otherEntityIterable);
if (attrs.size() != otherAttrs.size()) return false;
for (int i = 0; i < a... | java | public static boolean equalsEntities(
Iterable<Entity> entityIterable, Iterable<Entity> otherEntityIterable) {
List<Entity> attrs = newArrayList(entityIterable);
List<Entity> otherAttrs = newArrayList(otherEntityIterable);
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/model/Attribute.java | Attribute.getEnumOptions | public List<String> getEnumOptions() {
String enumOptionsStr = getString(ENUM_OPTIONS);
return enumOptionsStr != null ? asList(enumOptionsStr.split(",")) : emptyList();
} | java | public List<String> getEnumOptions() {
String enumOptionsStr = getString(ENUM_OPTIONS);
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/model/Attribute.java | Attribute.getInversedBy | public Attribute getInversedBy() {
// FIXME besides checking mappedBy attr name also check
// attr.getRefEntity().getFullyQualifiedName
if (hasRefEntity()) {
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// FIXME besides checking mappedBy attr name also check
// attr.getRefEntity().getFullyQualifiedName
if (hasRefEntity()) {
return Streams.stream(getRefEntity().getAtomicAttributes())
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molgenis/molgenis | molgenis-data-security/src/main/java/org/molgenis/data/security/auth/GroupPermissionService.java | GroupPermissionService.grantDefaultPermissions | public void grantDefaultPermissions(GroupValue groupValue) {
PackageIdentity packageIdentity = new PackageIdentity(groupValue.getRootPackage().getName());
GroupIdentity groupIdentity = new GroupIdentity(groupValue.getName());
aclService.createAcl(groupIdentity);
groupValue
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PackageIdentity packageIdentity = new PackageIdentity(groupValue.getRootPackage().getName());
GroupIdentity groupIdentity = new GroupIdentity(groupValue.getName());
aclService.createAcl(groupIdentity);
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/Fetch.java | Fetch.field | public Fetch field(String field, Fetch fetch) {
attrFetchMap.put(field, fetch);
return this;
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molgenis/molgenis | molgenis-genomebrowser/src/main/java/org/molgenis/genomebrowser/service/GenomeBrowserService.java | GenomeBrowserService.getTracksString | public List<String> getTracksString(Map<String, GenomeBrowserTrack> entityTracks) {
List<String> results = new ArrayList<>();
if (hasPermission()) {
Map<String, GenomeBrowserTrack> allTracks = new HashMap<>(entityTracks);
for (GenomeBrowserTrack track : entityTracks.values()) {
allTracks.put... | java | public List<String> getTracksString(Map<String, GenomeBrowserTrack> entityTracks) {
List<String> results = new ArrayList<>();
if (hasPermission()) {
Map<String, GenomeBrowserTrack> allTracks = new HashMap<>(entityTracks);
for (GenomeBrowserTrack track : entityTracks.values()) {
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molgenis/molgenis | molgenis-data-cache/src/main/java/org/molgenis/data/cache/l2/L2Cache.java | L2Cache.get | public Entity get(Repository<Entity> repository, Object id) {
LoadingCache<Object, Optional<Map<String, Object>>> cache = getEntityCache(repository);
EntityType entityType = repository.getEntityType();
return cache.getUnchecked(id).map(e -> entityHydration.hydrate(e, entityType)).orElse(null);
} | java | public Entity get(Repository<Entity> repository, Object id) {
LoadingCache<Object, Optional<Map<String, Object>>> cache = getEntityCache(repository);
EntityType entityType = repository.getEntityType();
return cache.getUnchecked(id).map(e -> entityHydration.hydrate(e, entityType)).orElse(null);
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molgenis/molgenis | molgenis-data-cache/src/main/java/org/molgenis/data/cache/l2/L2Cache.java | L2Cache.getBatch | public List<Entity> getBatch(Repository<Entity> repository, Iterable<Object> ids) {
try {
return getEntityCache(repository)
.getAll(ids)
.values()
.stream()
.filter(Optional::isPresent)
.map(Optional::get)
.map(e -> entityHydration.hydrate(e, reposit... | java | public List<Entity> getBatch(Repository<Entity> repository, Iterable<Object> ids) {
try {
return getEntityCache(repository)
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molgenis/molgenis | molgenis-data-cache/src/main/java/org/molgenis/data/cache/l2/L2Cache.java | L2Cache.createEntityCache | private LoadingCache<Object, Optional<Map<String, Object>>> createEntityCache(
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Repository<Entity> repository) {
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molgenis/molgenis | molgenis-data/src/main/java/org/molgenis/data/meta/EntityTypeRepositoryDecorator.java | EntityTypeRepositoryDecorator.removeMappedByAttributes | private void removeMappedByAttributes(Map<String, EntityType> resolvedEntityTypes) {
resolvedEntityTypes
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.filter(attribute -> resolvedEntityTypes.containsKey(attribute.getEntity().getId()))
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resolvedEntityTypes
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molgenis/molgenis | molgenis-jobs/src/main/java/org/molgenis/jobs/JobExecutionTemplate.java | JobExecutionTemplate.call | <T> T call(Job<T> job, Progress progress, JobExecutionContext jobExecutionContext) {
return runWithContext(jobExecutionContext, () -> tryCall(job, progress));
} | java | <T> T call(Job<T> job, Progress progress, JobExecutionContext jobExecutionContext) {
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molgenis/molgenis | molgenis-ontology/src/main/java/org/molgenis/ontology/sorta/service/impl/SortaServiceImpl.java | SortaServiceImpl.findSynonymWithHighestNgramScore | private Entity findSynonymWithHighestNgramScore(
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Iterable<Entity> entities =
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String cleanedQueryString = remove... | java | private Entity findSynonymWithHighestNgramScore(
String ontologyIri, String queryString, Entity ontologyTermEntity) {
Iterable<Entity> entities =
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molgenis/molgenis | molgenis-dataexplorer/src/main/java/org/molgenis/dataexplorer/negotiator/NegotiatorController.java | NegotiatorController.generateBase64Authentication | private static String generateBase64Authentication(String username, String password) {
requireNonNull(username, password);
String userPass = username + ":" + password;
String userPassBase64 = Base64.getEncoder().encodeToString(userPass.getBytes(UTF_8));
return "Basic " + userPassBase64;
} | java | private static String generateBase64Authentication(String username, String password) {
requireNonNull(username, password);
String userPass = username + ":" + password;
String userPassBase64 = Base64.getEncoder().encodeToString(userPass.getBytes(UTF_8));
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molgenis/molgenis | molgenis-r/src/main/java/org/molgenis/r/RScriptExecutor.java | RScriptExecutor.executeScriptExecuteRequest | private String executeScriptExecuteRequest(String rScript) throws IOException {
URI uri = getScriptExecutionUri();
HttpPost httpPost = new HttpPost(uri);
NameValuePair nameValuePair = new BasicNameValuePair("x", rScript);
httpPost.setEntity(new UrlEncodedFormEntity(singletonList(nameValuePair)));
S... | java | private String executeScriptExecuteRequest(String rScript) throws IOException {
URI uri = getScriptExecutionUri();
HttpPost httpPost = new HttpPost(uri);
NameValuePair nameValuePair = new BasicNameValuePair("x", rScript);
httpPost.setEntity(new UrlEncodedFormEntity(singletonList(nameValuePair)));
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molgenis/molgenis | molgenis-r/src/main/java/org/molgenis/r/RScriptExecutor.java | RScriptExecutor.executeScriptGetResponseRequest | private String executeScriptGetResponseRequest(
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String responseValue;
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String responseValue;
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@param outputPathname output pathname (can be null)
@return response value or null if scriptOutputFilename is not null
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molgenis/molgenis | molgenis-r/src/main/java/org/molgenis/r/RScriptExecutor.java | RScriptExecutor.executeScriptGetFileRequest | private void executeScriptGetFileRequest(
String openCpuSessionKey, String scriptOutputFilename, String outputPathname)
throws IOException {
URI scriptGetValueResponseUri =
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HttpGet httpGet = new HttpGet(scriptGetValueRespo... | java | private void executeScriptGetFileRequest(
String openCpuSessionKey, String scriptOutputFilename, String outputPathname)
throws IOException {
URI scriptGetValueResponseUri =
getScriptGetFileResponseUri(openCpuSessionKey, scriptOutputFilename);
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molgenis/molgenis | molgenis-r/src/main/java/org/molgenis/r/RScriptExecutor.java | RScriptExecutor.executeScriptGetValueRequest | private String executeScriptGetValueRequest(String openCpuSessionKey) throws IOException {
URI scriptGetValueResponseUri = getScriptGetValueResponseUri(openCpuSessionKey);
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String responseValue;
try (CloseableHttpResponse response = httpClient.exe... | java | private String executeScriptGetValueRequest(String openCpuSessionKey) throws IOException {
URI scriptGetValueResponseUri = getScriptGetValueResponseUri(openCpuSessionKey);
HttpGet httpGet = new HttpGet(scriptGetValueResponseUri);
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molgenis/molgenis | molgenis-core-ui/src/main/java/org/molgenis/core/ui/MolgenisWebAppConfig.java | MolgenisWebAppConfig.viewResolver | @Bean
public ViewResolver viewResolver() {
FreeMarkerViewResolver resolver = new FreeMarkerViewResolver();
resolver.setCache(true);
resolver.setSuffix(".ftl");
resolver.setContentType("text/html;charset=UTF-8");
return resolver;
} | java | @Bean
public ViewResolver viewResolver() {
FreeMarkerViewResolver resolver = new FreeMarkerViewResolver();
resolver.setCache(true);
resolver.setSuffix(".ftl");
resolver.setContentType("text/html;charset=UTF-8");
return resolver;
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molgenis/molgenis | molgenis-core-ui/src/main/java/org/molgenis/core/ui/MolgenisWebAppConfig.java | MolgenisWebAppConfig.freeMarkerConfigurer | @Bean
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public FreeMarkerConfigurer freeMarkerConfigurer() {
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molgenis/molgenis | molgenis-data-vcf/src/main/java/org/molgenis/data/vcf/format/VcfToEntity.java | VcfToEntity.toAttributeName | private String toAttributeName(String vcfInfoFieldKey) {
String attrName = infoFieldKeyToAttrNameMap.get(vcfInfoFieldKey);
if (attrName == null) {
throw new RuntimeException(
format("Missing attribute for VCF info field [%s]", vcfInfoFieldKey));
}
return attrName;
} | java | private String toAttributeName(String vcfInfoFieldKey) {
String attrName = infoFieldKeyToAttrNameMap.get(vcfInfoFieldKey);
if (attrName == null) {
throw new RuntimeException(
format("Missing attribute for VCF info field [%s]", vcfInfoFieldKey));
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molgenis/molgenis | molgenis-data-vcf/src/main/java/org/molgenis/data/vcf/format/VcfToEntity.java | VcfToEntity.determineVcfInfoFlagFields | private static Set<String> determineVcfInfoFlagFields(VcfMeta vcfMeta) {
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] | b4d0d6b27e6f6c8d7505a3863dc03b589601f987 | https://github.com/molgenis/molgenis/blob/b4d0d6b27e6f6c8d7505a3863dc03b589601f987/molgenis-data-vcf/src/main/java/org/molgenis/data/vcf/format/VcfToEntity.java#L433-L438 | train |
molgenis/molgenis | molgenis-data-vcf/src/main/java/org/molgenis/data/vcf/format/VcfToEntity.java | VcfToEntity.createInfoFieldKeyToAttrNameMap | private static Map<String, String> createInfoFieldKeyToAttrNameMap(
VcfMeta vcfMeta, String entityTypeId) {
Map<String, String> infoFieldIdToAttrNameMap =
newHashMapWithExpectedSize(size(vcfMeta.getInfoMeta()));
for (VcfMetaInfo info : vcfMeta.getInfoMeta()) {
// according to the VCF standar... | java | private static Map<String, String> createInfoFieldKeyToAttrNameMap(
VcfMeta vcfMeta, String entityTypeId) {
Map<String, String> infoFieldIdToAttrNameMap =
newHashMapWithExpectedSize(size(vcfMeta.getInfoMeta()));
for (VcfMetaInfo info : vcfMeta.getInfoMeta()) {
// according to the VCF standar... | [
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molgenis/molgenis | molgenis-data-cache/src/main/java/org/molgenis/data/cache/l1/L1Cache.java | L1Cache.get | public Optional<CacheHit<Entity>> get(String entityTypeId, Object id, EntityType entityType) {
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if (cache == null) {
return Optional.empty();
}
Optional<CacheHit<Entity>> result = cache.getIfPresent(entityType, id);
if (result.isPresent()) {
LOG.d... | java | public Optional<CacheHit<Entity>> get(String entityTypeId, Object id, EntityType entityType) {
CombinedEntityCache cache = caches.get();
if (cache == null) {
return Optional.empty();
}
Optional<CacheHit<Entity>> result = cache.getIfPresent(entityType, id);
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molgenis/molgenis | molgenis-data-cache/src/main/java/org/molgenis/data/cache/l1/L1Cache.java | L1Cache.put | public void put(String entityTypeId, Entity entity) {
CombinedEntityCache entityCache = caches.get();
if (entityCache != null) {
entityCache.put(entity);
LOG.trace(
"Added dehydrated row [{}] from entity {} to the L1 cache",
entity.getIdValue(),
entityTypeId);
}
} | java | public void put(String entityTypeId, Entity entity) {
CombinedEntityCache entityCache = caches.get();
if (entityCache != null) {
entityCache.put(entity);
LOG.trace(
"Added dehydrated row [{}] from entity {} to the L1 cache",
entity.getIdValue(),
entityTypeId);
}
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molgenis/molgenis | molgenis-data-cache/src/main/java/org/molgenis/data/cache/l1/L1CacheRepositoryDecorator.java | L1CacheRepositoryDecorator.findAllBatch | private List<Entity> findAllBatch(List<Object> batch) {
String entityId = getEntityType().getId();
EntityType entityType = getEntityType();
List<Object> missingIds =
batch
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String entityId = getEntityType().getId();
EntityType entityType = getEntityType();
List<Object> missingIds =
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molgenis/molgenis | molgenis-data-cache/src/main/java/org/molgenis/data/cache/l1/L1CacheRepositoryDecorator.java | L1CacheRepositoryDecorator.evictBiDiReferencedEntityTypes | private void evictBiDiReferencedEntityTypes() {
getEntityType().getMappedByAttributes().map(Attribute::getRefEntity).forEach(l1Cache::evictAll);
getEntityType()
.getInversedByAttributes()
.map(Attribute::getRefEntity)
.forEach(l1Cache::evictAll);
} | java | private void evictBiDiReferencedEntityTypes() {
getEntityType().getMappedByAttributes().map(Attribute::getRefEntity).forEach(l1Cache::evictAll);
getEntityType()
.getInversedByAttributes()
.map(Attribute::getRefEntity)
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molgenis/molgenis | molgenis-data-cache/src/main/java/org/molgenis/data/cache/l1/L1CacheRepositoryDecorator.java | L1CacheRepositoryDecorator.evictBiDiReferencedEntities | private void evictBiDiReferencedEntities(Entity entity) {
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molgenis/molgenis | molgenis-semantic-search/src/main/java/org/molgenis/semanticsearch/service/impl/SemanticSearchServiceImpl.java | SemanticSearchServiceImpl.findAttributes | public Hits<ExplainedAttribute> findAttributes(
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Iterable<String> attributeIdentifiers =
semanticSearchServiceHelper.getAttributeIdentifiers(sourceEntityType);
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EntityType sourceEntityType, Set<String> queryTerms, Collection<OntologyTerm> ontologyTerms) {
Iterable<String> attributeIdentifiers =
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molgenis/molgenis | molgenis-semantic-search/src/main/java/org/molgenis/semanticsearch/service/impl/SemanticSearchServiceImpl.java | SemanticSearchServiceImpl.createLexicalSearchQueryTerms | public Set<String> createLexicalSearchQueryTerms(
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Set<String> queryTerms = new HashSet<>();
if (searchTerms != null && !searchTerms.isEmpty()) {
queryTerms.addAll(searchTerms);
}
if (queryTerms.isEmpty()) {
if (StringUtils.isNotBl... | java | public Set<String> createLexicalSearchQueryTerms(
Attribute targetAttribute, Set<String> searchTerms) {
Set<String> queryTerms = new HashSet<>();
if (searchTerms != null && !searchTerms.isEmpty()) {
queryTerms.addAll(searchTerms);
}
if (queryTerms.isEmpty()) {
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molgenis/molgenis | molgenis-semantic-search/src/main/java/org/molgenis/semanticsearch/service/impl/SemanticSearchServiceImpl.java | SemanticSearchServiceImpl.convertAttributeToExplainedAttribute | public Set<ExplainedQueryString> convertAttributeToExplainedAttribute(
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EntityType attributeMetaData = dataService.getEntityType(ATTRIBUTE_META_DATA);
String attributeID = attribute.getIdentifier();
Explanation exp... | java | public Set<ExplainedQueryString> convertAttributeToExplainedAttribute(
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EntityType attributeMetaData = dataService.getEntityType(ATTRIBUTE_META_DATA);
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molgenis/molgenis | molgenis-data-import/src/main/java/org/molgenis/data/importer/PackageResolver.java | PackageResolver.resolvePackages | public static List<Entity> resolvePackages(Iterable<Entity> packageRepo) {
List<Entity> resolved = new LinkedList<>();
if ((packageRepo == null) || Iterables.isEmpty(packageRepo)) return resolved;
List<Entity> unresolved = new ArrayList<>();
Map<String, Entity> resolvedByName = new HashMap<>();
fo... | java | public static List<Entity> resolvePackages(Iterable<Entity> packageRepo) {
List<Entity> resolved = new LinkedList<>();
if ((packageRepo == null) || Iterables.isEmpty(packageRepo)) return resolved;
List<Entity> unresolved = new ArrayList<>();
Map<String, Entity> resolvedByName = new HashMap<>();
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molgenis/molgenis | molgenis-ontology-core/src/main/java/org/molgenis/ontology/core/repository/OntologyTermRepository.java | OntologyTermRepository.getOntologyTermDistance | public int getOntologyTermDistance(OntologyTerm ontologyTerm1, OntologyTerm ontologyTerm2) {
String nodePath1 = getOntologyTermNodePath(ontologyTerm1);
String nodePath2 = getOntologyTermNodePath(ontologyTerm2);
if (StringUtils.isEmpty(nodePath1)) {
throw new MolgenisDataAccessException(
"Th... | java | public int getOntologyTermDistance(OntologyTerm ontologyTerm1, OntologyTerm ontologyTerm2) {
String nodePath1 = getOntologyTermNodePath(ontologyTerm1);
String nodePath2 = getOntologyTermNodePath(ontologyTerm2);
if (StringUtils.isEmpty(nodePath1)) {
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molgenis/molgenis | molgenis-ontology-core/src/main/java/org/molgenis/ontology/core/repository/OntologyTermRepository.java | OntologyTermRepository.getChildren | public List<OntologyTerm> getChildren(OntologyTerm ontologyTerm) {
Iterable<org.molgenis.ontology.core.meta.OntologyTerm> ontologyTermEntities =
() ->
dataService
.query(ONTOLOGY_TERM, org.molgenis.ontology.core.meta.OntologyTerm.class)
.eq(ONTOLOGY_TERM_IRI, onto... | java | public List<OntologyTerm> getChildren(OntologyTerm ontologyTerm) {
Iterable<org.molgenis.ontology.core.meta.OntologyTerm> ontologyTermEntities =
() ->
dataService
.query(ONTOLOGY_TERM, org.molgenis.ontology.core.meta.OntologyTerm.class)
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molgenis/molgenis | molgenis-data-excel/src/main/java/org/molgenis/data/excel/ExcelUtils.java | ExcelUtils.toValue | static String toValue(Cell cell, List<CellProcessor> cellProcessors) {
String value;
switch (cell.getCellTypeEnum()) {
case BLANK:
value = null;
break;
case STRING:
value = cell.getStringCellValue();
break;
case NUMERIC:
if (DateUtil.isCellDateFormatted(... | java | static String toValue(Cell cell, List<CellProcessor> cellProcessors) {
String value;
switch (cell.getCellTypeEnum()) {
case BLANK:
value = null;
break;
case STRING:
value = cell.getStringCellValue();
break;
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"(",
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"null",... | Gets a cell value as String and process the value with the given cellProcessors | [
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] | b4d0d6b27e6f6c8d7505a3863dc03b589601f987 | https://github.com/molgenis/molgenis/blob/b4d0d6b27e6f6c8d7505a3863dc03b589601f987/molgenis-data-excel/src/main/java/org/molgenis/data/excel/ExcelUtils.java#L35-L124 | train |
molgenis/molgenis | molgenis-data-excel/src/main/java/org/molgenis/data/excel/ExcelUtils.java | ExcelUtils.formatUTCDateAsLocalDateTime | private static String formatUTCDateAsLocalDateTime(Date javaDate) {
// Now back from start of day in UTC to LocalDateTime to express that we don't know the
// timezone.
LocalDateTime localDateTime = javaDate.toInstant().atZone(UTC).toLocalDateTime();
// And format to string
return localDateTime.toSt... | java | private static String formatUTCDateAsLocalDateTime(Date javaDate) {
// Now back from start of day in UTC to LocalDateTime to express that we don't know the
// timezone.
LocalDateTime localDateTime = javaDate.toInstant().atZone(UTC).toLocalDateTime();
// And format to string
return localDateTime.toSt... | [
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@param javaDate Parsed Date representing start of day in UTC
@return Formatted {@link LocalDateTime} string of the java.util.Date | [
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molgenis/molgenis | molgenis-core-ui/src/main/java/org/molgenis/core/ui/MolgenisUiUtils.java | MolgenisUiUtils.getCurrentUri | public static String getCurrentUri() {
HttpServletRequest request =
((ServletRequestAttributes) RequestContextHolder.currentRequestAttributes()).getRequest();
StringBuilder uri = new StringBuilder();
uri.append(request.getAttribute("javax.servlet.forward.request_uri"));
if (StringUtils.isNotBl... | java | public static String getCurrentUri() {
HttpServletRequest request =
((ServletRequestAttributes) RequestContextHolder.currentRequestAttributes()).getRequest();
StringBuilder uri = new StringBuilder();
uri.append(request.getAttribute("javax.servlet.forward.request_uri"));
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<p>Must be used in a Spring environment | [
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